Microbiota-mediated colonization resistance: mechanisms and regulation

A core gut microbiome in obese and lean twins

Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., et al. (2009) · Nature · doi:10.1038/nature07540 · Cited by 7,823

Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns

Dominguez-Bello, M. G., Costello, E. K., Contreras, M., Magris, M., Hidalgo, G., Fierer, N., & Knight, R. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1002601107 · Cited by 4,774

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

Ivanov, I. I., Atarashi, K., Manel, N., Brodie, E. L., Shima, T., Karaoz, U., Wei, D., Goldfarb, K. C., Santee, C. A., Lynch, S. V., et al. (2009) · Cell · doi:10.1016/j.cell.2009.09.033 · Cited by 4,554

Vaginal microbiome of reproductive-age women

Ravel, J., Gajer, P., Abdo, Z., Schneider, G. M., Koenig, S. S. K., McCulle, S. L., Karlebach, S., Gorle, R., Russell, J., Tacket, C. O., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1002611107 · Cited by 4,254

The impact of the gut microbiota on human health: an integrative view

Clemente, J. C., Ursell, L. K., Parfrey, L. W., & Knight, R. (2012) · Cell · doi:10.1016/j.cell.2012.01.035 · Cited by 3,710

Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile

van Nood, E., Vrieze, A., Nieuwdorp, M., Fuentes, S., Zoetendal, E. G., de Vos, W. M., Visser, C. E., Kuijper, E. J., Bartelsman, J. F. W. M., Tijssen, J. G. P., et al. (2013) · New England Journal of Medicine · doi:10.1056/nejmoa1205037 · Cited by 3,708

Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life

Bäckhed, F., Roswall, J., Peng, Y., Feng, Q., Jia, H., Kovatcheva-Datchary, P., Li, Y., Xia, Y., Xie, H., Zhong, H., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.04.004 · Cited by 3,315

Topographical and Temporal Diversity of the Human Skin Microbiome

Grice, E. A., Kong, H. H., Conlan, S., Deming, C. B., Davis, J., Young, A. C., Program, N. C. S., Bouffard, G. G., Blakesley, R. W., Murray, P. R., et al. (2009) · Science · doi:10.1126/science.1171700 · Cited by 2,953

A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility

Desai, M. S., Seekatz, A. M., Koropatkin, N. M., Kamada, N., Hickey, C. A., Wolter, M., Pudlo, N. A., Kitamoto, S., Terrapon, N., Muller, A., et al. (2016) · Cell · doi:10.1016/j.cell.2016.10.043 · Cited by 2,805

The NIH Human Microbiome ProjectPreprint

The NIH HMP Working Group, Peterson, J. L., Garges, S., Giovanni, M. Y., McInnes, P., Wang, L., Schloss, J. A., Bonazzi, V. R., McEwen, J. E., Wetterstrand, K. A., et al. (2009) · Genome Research · doi:10.1101/gr.096651.109 · Cited by 2,168

Dietary amino acids regulate Salmonella colonization via microbiota-dependent mechanisms in the mouse gut

Pickard, J. M., Porwollik, S., Caballero-Flores, G. G., Caruso, R., Fukuda, S., Soga, T., Inohara, N., McClelland, M., & Núñez, G. (2025) · Nature Communications · doi:10.1038/s41467-025-59706-1 · Cited by 17

Polyketide synthase-derived sphingolipids mediate microbiota protection against a bacterial pathogen in C. elegans

Peters, L., Drechsler, M., Herrera, M. A., Liu, J., Pees, B., Jarstorff, J., Czerwinski, A., Lubbock, F., Angelidou, G., Salzer, L., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-60234-1 · Cited by 14

Skin microbiota in atopic dermatitis: victim or executioner?

Boggio, C. M. T., Veronese, F., Armari, M., Zavattaro, E., Esposto, E., Savoia, P., & Azzimonti, B. (2025) · Clinical Microbiology Reviews · doi:10.1128/cmr.00277-24 · Cited by 14

Incorporating microbiomes into the One Health Joint Plan of Action

Couradeau, E., Martiny, J. B. H., Fontaine, F., Bréchot, C., Bonneville, M., Callens, K., Initiative, T. M. F. O. H., Asnicar, F., Baker, B. J., Berg, G., et al. (2025) · mBio · doi:10.1128/mbio.01456-25 · Cited by 17

Neutrophil recruitment during intestinal inflammation primes Salmonella elimination by commensal E. coli in a context-dependent manner

Cherrak, Y., Younes, A. A., Perez‐Molphe‐Montoya, E., Maurer, L., Yilmaz, K., Enz, U., Zeder, C., Kiefer, P., Christen, P., Gül, E., et al. (2025) · Cell Host & Microbe · doi:10.1016/j.chom.2025.02.004 · Cited by 13

Leveraging microbial ecology for mosquito-borne disease control

Nichols, H. L., & Coon, K. L. (2025) · Trends in Parasitology · doi:10.1016/j.pt.2025.06.010 · Cited by 13

Ecology of the gut microbiota and colonization resistance: mechanisms and therapeutic implications

Liang, L., Yang, Z., & Fu, X. (2025) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiaf124 · Cited by 14

The Gut Microbiota-Brain Axis: A New Frontier in Alzheimer's Disease Pathology

Dhanawat, M., Garima, G., Wilson, K., Gupta, S., Gupta, N., & Sardana, S. (2024) · CNS & Neurological Disorders - Drug Targets · doi:10.2174/0118715273302508240613114103 · Cited by 13

A review of gut microbial metabolites and therapeutic approaches in hypertension

Olalekan, S. O., Bakare, O. O., Faponle, A. S., & Okwute, P. G. (2024) · Bulletin of the National Research Centre/Bulletin of the National Research Center · doi:10.1186/s42269-024-01252-9 · Cited by 12

The microbiome’s influence on obesity: mechanisms and therapeutic potential

Tadese, D. A., Mwangi, J., Luo, L., Zhang, H., Huang, X., Michira, B. B., Zhou, S., Kamau, P. M., Lu, Q., & Lai, R. (2024) · Science China Life Sciences · doi:10.1007/s11427-024-2759-3 · Cited by 21

Changes in the gut microbiome due to diarrhea in neonatal Korean indigenous calves

Ku, J., Lee, M.-J., Jung, Y., Choi, H., & Park, J. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1511430 · Cited by 12

Intestinal microecology dysbiosis in inflammatory bowel disease: Pathogenesis and therapeutic strategies

Yin, Y., Feng, W., Chen, X., Chen, J., Wang, G., Xia, L., & Wu, K. (2024) · The Innovation Medicine · doi:10.59717/j.xinn-med.2024.100092 · Cited by 11

The occurrence of Aerococcus urinaeequi and non-aureus staphylococci in raw milk negatively correlates with Escherichia coli clinical mastitis

Jung, D., Park, S., Kurban, D., Dufour, S., & Ronholm, J. (2024) · mSystems · doi:10.1128/msystems.00362-24 · Cited by 11

Metagenomic profiling of cecal microbiota and antibiotic resistome in rodents

Shang, K.-M., Elsheikha, H. M., Ma, H., Wei, Y.-J., Zhao, J., Qin, Y., Li, J., Zhao, Z., & Zhang, X. (2024) · Ecotoxicology and Environmental Safety · doi:10.1016/j.ecoenv.2024.117186 · Cited by 11

Klebsiella oxytoca facilitates microbiome recovery via antibiotic degradation and restores colonization resistance in a diet-dependent manner

Almási, É. D. H., Eisenhard, L., Osbelt, L., Lesker, T. R., Vetter, A. C., Knischewski, N., Bielecka, A. A., Gronow, A., Muthukumarasamy, U., Wende, M., et al. (2025) · Nature Communications · doi:10.1038/s41467-024-55800-y · Cited by 13

The Human Superorganism: Using Microbes for Freedom vs. Fear

Dietert, R. R., & Dietert, J. M. (2023) · Applied Microbiology · doi:10.3390/applmicrobiol3030061 · Cited by 12

A new in vivo model of intestinal colonization using Zophobas morio larvae: testing hyperepidemic ESBL- and carbapenemase-producing Escherichia coli clones

Eddoubaji, Y., Aldeia, C., Campos-Madueno, E. I., Moser, A. I., Kundlacz, C., Perreten, V., Hilty, M., & Endimiani, A. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1381051 · Cited by 11

Host-microbiota interactions in genitourinary cancer immunotherapy

Xu, X., Cui, J., Li, W., Xu, Y., Yuan, S., Zeng, X., & Li, B. (2025) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2025.07.005 · Cited by 11

Phenotype Alterations in the Cecal Ecosystem Involved in the Asymptomatic Intestinal Persistence of Paratyphoid Salmonella in Chickens

Kogut, M. H., & Fernández-Miyakawa, M. E. (2023) · Animals · doi:10.3390/ani13182824 · Cited by 11

Molecular characterization of Pasteurella multocida from cats and antibiotic sensitivity of the isolates

Ziagham, A., Gharibi, D., Mosallanejad, B., & Avizeh, R. (2024) · Veterinary Medicine and Science · doi:10.1002/vms3.1424 · Cited by 10

Faecalibacterium prausnitzii A2-165 metabolizes host- and media-derived chemicals and induces transcriptional changes in colonic epithelium in GuMI human gut microphysiological system

Huang, Y.-J., Lewis, C. A., Wright, C. W., Schneider, K., Kemmitt, J., Trumper, D. L., Breault, D. T., Yilmaz, Ö. H., Griffith, L. G., & Zhang, J. (2024) · Microbiome Research Reports · doi:10.20517/mrr.2024.14 · Cited by 10

A master regulator of central carbon metabolism directly activates virulence gene expression in attaching and effacing pathogens

Wale, K. R., O’Boyle, N., McHugh, R. E., Serrano, E., Mark, D. R., Douce, G. R., Connolly, J. P. R., & Roe, A. J. (2024) · PLoS Pathogens · doi:10.1371/journal.ppat.1012451 · Cited by 10

Evaluating the Efficacy of Secondary Metabolites in Antibiotic-Induced Dysbiosis: A Narrative Review of Preclinical Studies

Andrei, C., Zanfirescu, A., Ormeneanu, V.-P., & Negreș, S. (2025) · Antibiotics · doi:10.3390/antibiotics14020138 · Cited by 11

Phosphole-Based Fluorescent Biomaterials for Imaging and Therapy

Zhuang, Z., Li, J., Tang, B. Z., & Zhao, Z. (2025) · Chemical & Biomedical Imaging · doi:10.1021/cbmi.4c00096 · Cited by 10

Dietary intake of enrofloxacin promotes the spread of antibiotic resistance from food to simulated human gut

Wang, Q., Liu, C., Sun, Y., Li, X., Gu, W., Wang, N., Sun, S., & Luo, Y. (2025) · The ISME Journal · doi:10.1093/ismejo/wraf045 · Cited by 10

Breed-specific responses to coccidiosis in chickens: identification of intestinal bacteria linked to disease resistance

Broadwater, C., Guo, J., Liu, J., Tobin, I., Whitmore, M. A., Kaiser, M. G., Lamont, S. J., & Zhang, G. (2025) · Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology · doi:10.1186/s40104-025-01202-z · Cited by 12

Using the microbiota to study connectivity at human–animal interfaces

Muloi, D. M., Caron, A., Berkley, J. A., Hassell, J. M., Brito, I., King, K. C., Moodley, A., & Fèvre, E. M. (2025) · Trends in Microbiology · doi:10.1016/j.tim.2025.05.006 · Cited by 12

Multi-omics analyses reveal altered gut microbial thiamine production in obesity

Xia, Y., Lu, L., Wang, L., Qiu, Y., Liu, X., & Ge, W. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1516393 · Cited by 11

Strain-specific galactose utilization by commensal E. coli mitigates Salmonella establishment in the gut

Schubert, C., Näf, J., Petukhov, L., Laganenka, L., Cherrak, Y., & Hardt, W. (2025) · PLoS Pathogens · doi:10.1371/journal.ppat.1013232 · Cited by 12

Crop genotype modulates root rot resistance-associated microbial community composition and abundance of key taxa

Gfeller, V., Schneider, M. C., Bodenhausen, N., Horton, M., Wille, L., Oldach, K., Studer, B., Hartmann, M., Messmer, M., & Hohmann, P. (2025) · Environmental Microbiome · doi:10.1186/s40793-025-00755-w · Cited by 10

The impact of three carbapenems at a single-day dose on intestinal colonization resistance against carbapenem-resistant Klebsiella pneumoniae

Kuang, H., Yang, Y., Luo, H., & Lv, X. (2023) · mSphere · doi:10.1128/msphere.00479-23 · Cited by 11

Microbial Interventions to Improve Neonatal Gut Health

Nakandalage, R., Guan, L. L., & Malmuthuge, N. (2023) · Microorganisms · doi:10.3390/microorganisms11051328 · Cited by 10

Lacticaseibacillus rhamnosus P118 enhances host tolerance to Salmonella infection by promoting microbe-derived indole metabolitesPreprint

Wang, B., Peng, X., Zhou, X. W., Jin, X., Siddique, A., Yao, J., Zhang, H., Li, Y., Li, Y., & Yue, M. (2024) · eLife · doi:10.7554/elife.101198 · Cited by 11

Distinct members of the Caenorhabditis elegans CeMbio reference microbiota exert cryptic virulence that is masked by host defense

Gonzalez, X., & Irazoqui, J. E. (2024) · Molecular Microbiology · doi:10.1111/mmi.15258 · Cited by 9

Pre- to Postbiotics: The Beneficial Roles of Pediatric Dysbiosis Associated with Inflammatory Bowel Diseases

Ottria, R., Xynomilakis, O., Casati, S., & Ciuffreda, P. (2024) · Microorganisms · doi:10.3390/microorganisms12081582 · Cited by 9

Modeling the effects of prebiotic interventions on luminal and mucosa-associated gut microbiota without and with Clostridium difficile challenge in vitro

Wiese, M., van der Wurff, M., Ouwens, A. M. T., van Leijden, B., Verheij, E. R., Heerikhuisen, M., & van der Vossen, J. M. B. M. (2024) · Frontiers in Nutrition · doi:10.3389/fnut.2024.1403007 · Cited by 11

Evaluating the Effects of Sugar Shift® Symbiotic on Microbiome Composition and LPS Regulation: A Double-Blind, Placebo-Controlled Study

García, G., Soto, J., Netherland, M., Hasan, N. A., Faxas, E. B., Martínez, D., Carlin, M. R., & Cano, R. J. (2024) · Microorganisms · doi:10.3390/microorganisms12122525 · Cited by 11

An RNase III–processed sRNA coordinates sialic acid metabolism of Salmonella enterica during gut colonization

Chen, Z., Yang, Y., Chen, X., Bei, C., Gao, Q., Chao, Y., & Wang, C. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2414563122 · Cited by 9

Role of gut microbiota in predicting chemotherapy-induced neutropenia duration in leukemia patients

Huang, Y., Liao, L., Jiang, Y., Tao, S., & Tang, D. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1507336 · Cited by 9

Link Between Oral and Gut Microbiomes: The Oral–Gut Axis

Colombo, A. P. V., Lourenço, T. G. B., de Oliveira, A. M., & da Costa, A. L. A. (2025) · Advances in experimental medicine and biology · doi:10.1007/978-3-031-79146-8_5 · Cited by 10

Genetically engineered plant endophytes broaden effector-triggered immunity

Hou, M., Zhu, S., Niu, R., Zhong, G., Wang, Z., Luo, M., Long, J., Yang, R., Tang, Z., Shi, S., et al. (2025) · Cell Host & Microbe · doi:10.1016/j.chom.2025.09.017 · Cited by 9

The exploitation of nutrient metals by bacteria for survival and infection in the gut

Bushman, S. D., & Skaar, E. P. (2025) · PLoS Pathogens · doi:10.1371/journal.ppat.1013580 · Cited by 11

Design and application of synthetic human gut microbial communities

Kim, M. S., & Bisanz, J. E. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2575923 · Cited by 10

A host-centric view of the microbiota metabolome

Yamada, T., & Palm, N. W. (2025) · Immunity · doi:10.1016/j.immuni.2025.11.006 · Cited by 12

High-resolution lineage tracking of within-host evolution and strain transmission in a human gut symbiont across ecological scalesPreprint

Vasquez, K. S., Wong, D. P. G. H., Pedro, M. F., Yu, F. B., Jain, S., Meng, X., Higginbottom, S. K., DeFelice, B. C., Neff, N. F., Bhatt, A. S., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.17.580834 · Cited by 9

Quantification of gut microbiome metabolites using chemical isotope derivatization strategy combined with LC-MS/MS: Application in neonatal hypoxic-ischemic encephalopathy rat model

Xia, F., Cui, P., Liu, L., Chen, J., Zhou, Q.-Q., Wang, Q., & Zhou, H. (2024) · Journal of Pharmaceutical and Biomedical Analysis · doi:10.1016/j.jpba.2024.116312 · Cited by 9

Effect of β-lactam antibiotics on the gut microbiota of term neonates

Gu, H., Tao, E., Fan, Y., Long, G., Jia, X., Yuan, T., Chen, L., Shu, X., Zheng, W., & Jiang, M. (2024) · Annals of Clinical Microbiology and Antimicrobials · doi:10.1186/s12941-024-00730-2 · Cited by 8

Multi-omics reveals the ecological and biological functions of Enterococcus mundtii in the intestine of lepidopteran insects

Li, G., Wu, M., Xiao, Y., Tong, Y., Li, S., Qian, H., & Zhao, T. (2024) · Comparative Biochemistry and Physiology Part D Genomics and Proteomics · doi:10.1016/j.cbd.2024.101309 · Cited by 8

Synthetic bacterial consortia transplantation attenuates vaginal inflammation and modulates the immune response in a mouse model of Gardnerella vaginalis-induced bacterial vaginosis

Liu, Y., He, L., Hu, Y. P., Liao, X., Wang, H., & Yang, L. (2024) · Heliyon · doi:10.1016/j.heliyon.2024.e38218 · Cited by 9

Core symbionts, age at inoculation and diet affect colonization of the bumblebee gut by a common bacterial pathogen

Nelson, A. S., Larson, M. J., & Hammer, T. J. (2025) · Journal of Animal Ecology · doi:10.1111/1365-2656.70029 · Cited by 9

A consortium of seven commensal bacteria promotes gut microbiota recovery and strengthens ecological barrier against vancomycin-resistant enterococci

Jan, A., Bayle, P., Mohellibi, N., Lemoine, C., Pepke, F., Béguet-Crespel, F., Jouanin, I., Tremblay‐Franco, M., Laroche, B., Serror, P., et al. (2025) · Microbiome · doi:10.1186/s40168-025-02127-5 · Cited by 8

Working together: gut microbe-microbe interactions shape host inflammation

Lawing, A., & Bleich, R. M. (2025) · Infection and Immunity · doi:10.1128/iai.00512-24 · Cited by 8

Molecular mechanisms of co-infections

Walch, P., & Brož, P. (2025) · EMBO Reports · doi:10.1038/s44319-025-00517-2 · Cited by 8

Understanding microbiome shifts and their impacts on plant health during pathogen infections

Thomazella, D. P. D. T., Pereira, L. B., & Teixeira, P. J. P. L. (2025) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiaf498 · Cited by 8

Microbiota and inflammatory bowel disease: the dual effect mechanism of polysaccharide therapy

Yang, J., Huang, Q., Long, J., & Jia, L. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1666866 · Cited by 13

Klebsiella ARO112 promotes microbiota recovery, pathobiont clearance and prevents inflammation in IBD mice

Cabral, V., Oliveira, R. A., Correia, M. B., Pedro, M. F., Garcia‐Garcerà, M., Úbeda, C., & Xavier, K. B. (2025) · Nature Communications · doi:10.1038/s41467-025-67015-w · Cited by 11

Gut microbiome alpha diversity decreases in relation to body weight, antibiotic exposure, and infection with multidrug-resistant organisms

Panzer, J. J., Maples, C., Meyer, M. P., Tillotson, G., Theis, K. R., & Chopra, T. (2024) · American Journal of Infection Control · doi:10.1016/j.ajic.2023.12.017 · Cited by 8

The role of gut microbiota associated metabolites in digestive disorders

Li, N., Zhao, C., Zhang, P., Wu, S., Dou, X., Xu, S., Zhang, X., Peng, C., Xie, Y., Huang, S., et al. (2024) · Engineered Regeneration · doi:10.1016/j.engreg.2024.04.003 · Cited by 9

Enterococcus faecalis-derived adenine enhances enterohaemorrhagic Escherichia coli Type 3 Secretion System-dependent virulence

Martins, F. H., Rosay, T., Rajan, A., Carter, H. E., Turocy, T., Mejia, A. F., Crawford, J. M., Maresso, A. W., & Sperandio, V. (2024) · Nature Microbiology · doi:10.1038/s41564-024-01747-1 · Cited by 11

Bowel preparation before colonoscopy: Consequences, mechanisms, and treatment of intestinal dysbiosis

Zheng, Z.-L., Zheng, Q.-F., Wang, L., & Liu, Y. (2024) · World Journal of Gastroenterology · doi:10.3748/wjg.v31.i2.100589 · Cited by 9

Uropathogenic Escherichia coli niche occupancy determines the effects of mucosal vaccine against FimH

Santiago-Borges, J. M., Rosen, A. L., Hernandez-Leyva, A. J., Tomera, C. P., Lint, M. A., Paharik, A. E., Vanyo, V., Pinkner, J. S., Dodson, K., Chen, S. L., et al. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.116077 · Cited by 7

How nutrient starvation impacts the gut microbiome

Estrela, S., Long, J. Z., & Huang, K. C. (2025) · Nature Microbiology · doi:10.1038/s41564-025-02139-9 · Cited by 11

A review on the ecological niche and functional properties of enterococci in health promotion

He, Y., Liu, Z., Huang, Y., Qiu, L., Tao, X., & Wei, H. (2025) · Current Research in Food Science · doi:10.1016/j.crfs.2025.101211 · Cited by 7

Prevotella copri alleviates diarrhea in weaning piglets through gut microbiota modulation and arachidonic acid–AHR–NRF2 pathway activation

Lan, C., Ren, W., Wu, A., Yu, B., He, J., Luo, Y., & Chen, D. (2025) · Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology · doi:10.1186/s40104-025-01273-y · Cited by 9

A synthetic Glutamicibacter consortium efficiently removes ammonium and nitrite from aquaculture wastewater

Su, X., Lu, J. F., Jiang, Y., Liu, F., Zhong, C., Yang, M., Zhang, H., Cui, J., & Meng, H. (2025) · Bioresource Technology · doi:10.1016/j.biortech.2025.133683 · Cited by 7

Tumor-associated high endothelial venules as therapeutic modulation targets in cancer immunotherapy

Zhang, J.-Y., Piao, Z.-Y., Su, G.-L., Zhang, M.-J., & Sun, Z. (2025) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2025.189500 · Cited by 8

Non-antibiotic drugs break colonization resistance against pathogenic GammaproteobacteriaPreprint

Grießhammer, A., de la Cuesta‐Zuluaga, J., Zahir, T., Müller, P., Gekeler, C., Chang, H., Schmitt, K., Planker, C., Bohn, E., Nguyen, T. H., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.11.06.564936 · Cited by 7

IL-17RA–Mediated Epithelial Cell Activity Prevents Severe Inflammatory Response to Helicobacter pylori Infection

Brackman, L. C., Jung, M. S., Ogaga, E., Joshi, N., Wroblewski, L. E., Piazuelo, M. B., Peek, R. M., Choksi, Y. A., & Algood, H. M. S. (2024) · ImmunoHorizons · doi:10.4049/immunohorizons.2300078 · Cited by 6

Determinants of raffinose family oligosaccharide use in Bacteroides species

Basu, A., Adams, A. N. D., Degnan, P. H., & Vanderpool, C. K. (2024) · Journal of Bacteriology · doi:10.1128/jb.00235-24 · Cited by 6

Symbiosis Between the Oral Microbiome and the Human Host: Microbial Homeostasis and Stability of the Host

Santos, H. S. D. B., Pagnussatti, M. E. L., & Arthur, R. A. (2025) · Advances in experimental medicine and biology · doi:10.1007/978-3-031-79146-8_3 · Cited by 7

Metabolites derived from bacterial isolates of the human skin microbiome inhibit Staphylococcus aureus biofilm formation

Le, V. T. M., King, T., Wuerzberger, B., Bauer, O. R., Carver, M. N., Chan, T. S., Henson, A. L., Hubbard, G. K., Kopadze, T., Patterson, C. F., et al. (2025) · Microbiology Spectrum · doi:10.1128/spectrum.01306-25 · Cited by 6

Synergistic effects of commensals and phage predation in suppressing colonization by pathogenic Vibrio parahaemolyticus

Chen, L., Huang, Z., Middelboe, M., Deng, D., & Ma, Y. (2025) · npj Biofilms and Microbiomes · doi:10.1038/s41522-025-00802-x · Cited by 7

Understanding Probiotics, Prebiotics, Synbiotics, and Postbiotics: A Comprehensive Review of the Newest Definitions, Selected Strains and Products

Woźniak, A., Dorotkiewicz‐Jach, A., & Brzychczy‐Włoch, M. (2025) · Postępy Mikrobiologii - Advancements of Microbiology · doi:10.2478/am-2025-0013 · Cited by 8

Unveiling the interplay between microbiota and PD1/PD-L1 axis in tumor immunity and immunotherapy

Lu, Q., Wu, J., Yu, X., Qian, J., & Song, Z. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1690374 · Cited by 6

Fecal microbial and metabolic signatures in children with very early onset inflammatory bowel disease

Kvitne, K. E., Zuffa, S., Charron‐Lamoureux, V., Mohanty, I., Patan, A., Mannochio-Russo, H., Zemlin, J., Burnett, L. A., Zhang, L. S., Cecala, M., et al. (2025) · npj Biofilms and Microbiomes · doi:10.1038/s41522-025-00899-0 · Cited by 6

Broad-spectrum antibiotic treatment reshapes the gut microbiome, resistome, and colonization potential of opportunistic pathogens: a metagenomics study

Tigabu, A., & Leung, P. H. M. (2026) · Gut Pathogens · doi:10.1186/s13099-026-00795-8 · Cited by 8

Phage-steering permits antibody-mediated clearance of E. coli K1 from the gut

Larsson, L., Bertola, A., Wenner, N., Kaur, J., Dion, S., Rocha, L. F. L., Keys, T. G., Rutschmann, C., Vershynina, K., Dimakou, D., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-70808-2 · Cited by 6

The gut microbiome as a rainforest: probiotic colonization resistance, functional effects, and next-generation strategies

Lewandowski, R. (2026) · FEMS Microbiology Letters · doi:10.1093/femsle/fnag035 · Cited by 6

Probiotics and the Risk of Infection

Younge, N. E., & Patel, R. M. (2024) · Clinics in Perinatology · doi:10.1016/j.clp.2024.10.006 · Cited by 6

Hosts and Commensal Bacteria Synergistically Antagonize Opportunistic Pathogens at the Single‐Cell Resolution

Zhang, S., Wang, Z., Liu, A., Li, J., Zhuang, J., Ji, X., Mulama, P. I., Li, M., Cao, H., Tan, E., et al. (2025) · Advanced Science · doi:10.1002/advs.202500582 · Cited by 8

From wolves to humans: oral microbiome resistance to transfer across mammalian hosts

Podar, N. A., Carrell, A. A., Cassidy, K. A., Klingeman, D. M., Yang, Z. K., Stahler, E. E., Smith, D. W., Stahler, D. R., & Podar, M. (2024) · mBio · doi:10.1128/mbio.03342-23 · Cited by 8

Commensal lifestyle regulated by a negative feedback loop between Arabidopsis ROS and the bacterial T2SSPreprint

Entila, F. D., Han, X., Mine, A., Schulze‐Lefert, P., & Tsuda, K. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.05.09.539802 · Cited by 6

Odoribacter splanchnicus mitigates pathogen - induced gut inflammation and its associated pathogenesis via its secreted bacteriocinPreprint

Hajra, D., Mukherjee, D., Vij, R., Rajmani, R. S., Dadireddy, V., Das, D., Hussain, T., Ganji, M., Tatu, U. S., & Chakravortty, D. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.08.23.609322 · Cited by 5

Tyrosine availability shapes Staphylococcus aureus nasal colonization and interactions with commensal communitiesPreprint

Camus, L., Franz, J., Gerlach, D., Lange, A., Power, J. J., Navarro-Díaz, M., Rapp, J., Otto, M., Klages, L. J., Starostin, V., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.06.651429 · Cited by 7

Inulin protects against the harmful effects of dietary emulsifiers on mice gut microbiome

Bekar, C., Özmen, Ö., Özkul, C., & Ayaz, A. (2024) · PeerJ · doi:10.7717/peerj.17110 · Cited by 6

Helicobacter pylori Pathogenic Factors and Their Interactions With the Gastric Microbiome

Savitri, C. M. A., Matsumoto, T., Fauzia, K. A., Alfaray, R. I., Waskito, L. A., Rezkitha, Y. A. A., Uchida, T., Miftahussurur, M., & Yamaoka, Y. (2025) · Helicobacter · doi:10.1111/hel.70072 · Cited by 5

The Role of the Microbiome in the Resolution of Infection-Induced Inflammation

McGowen, K., Lee, J., & Pedicord, V. A. (2025) · ACS Infectious Diseases · doi:10.1021/acsinfecdis.5c00668 · Cited by 6

Phytate enhances gut Parasutterella colonization to alleviate radiation injury

Li, Y., Qiu, J., Liu, Z., Xiao, H., Wang, B., Dong, Y., Xiao, Y., Wang, Q., Dong, J., & Cui, M. (2025) · Cell chemical biology · doi:10.1016/j.chembiol.2025.10.009 · Cited by 5

Commensal microflora coating endows implants with biofilm-repellent, immunomodulatory and osteogenic properties

Rahim, M. I., Baseer, S., Paasch, D., Steglich, M., Waqas, S. F., Lachmann, N., Falk, C. S., & Stiesch, M. (2026) · Acta Biomaterialia · doi:10.1016/j.actbio.2026.01.017 · Cited by 5

Dynamics of the gut and lung microbiota in severe infections: from observational studies to therapeutic strategies

Fortman, D. P. E. D. G., Kullberg, R. F. J., Wiersinga, W. J., & Haak, B. W. (2026) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2026.02.016 · Cited by 7

Probiotic Therapy with Lactobacillus Restores Gut Microbiota and Modulates Immunity in Salmonella -Infected Mice

Junaid, M., Lu, H., Li, Y., Liu, Y., Qi, Z. Q., Liu, K., & Yan, J. (2026) · Foodborne Pathogens and Disease · doi:10.1177/15353141261430303 · Cited by 5

Dissemination of ESBL-producing Escherichia coli and carriage in the community worldwide: epidemiology, transmission pathways, molecular insights, and practical aspects

Beaumont, A., Danjean, M., Jacquier, H., Boyd, A. C., Jaspard, M., Royer, G., Surgers, L., & Woerther, P. (2026) · Clinical Microbiology Reviews · doi:10.1128/cmr.00274-25 · Cited by 7

Health‐promoting worms? Prospects and pitfalls of helminth therapy

Lamminpää, I., Boem, F., & Amedei, A. (2024) · BioEssays · doi:10.1002/bies.202400080 · Cited by 5

Role of nasal microbiota in regulating host anti-influenza immunity in dogs

Geng, J., Dong, Y., Huang, H., Wen, X., Xu, T., Zhao, Y., & Liu, Y. (2025) · Microbiome · doi:10.1186/s40168-025-02031-y · Cited by 6

Lacticaseibacillus rhamnosus P118 enhances host tolerance to Salmonella infection by promoting microbe-derived indole metabolites

Wang, B., Peng, X., Zhou, X., Jin, X., Siddique, A., Yao, J., Zhang, H., Li, W., Li, Y., & Yue, M. (2025) · eLife · doi:10.7554/elife.101198.4 · Cited by 5

The health benefits of dietary polyphenols on pediatric intestinal diseases: Mechanism of action, clinical evidence and future research progress

Jiang, Y., liu, R., Tang, J. H., Li, M., Zhang, D., Pei, Z., Fan, S., Xu, R., Huang, H., & Lin, J. (2024) · Phytotherapy Research · doi:10.1002/ptr.8218 · Cited by 5

Using In Vitro Models to Study the Interactions Between Environmental Exposures and Human Microbiota

Cheng, Q., & Chen, S. (2025) · Microorganisms · doi:10.3390/microorganisms13020247 · Cited by 6

Monosaccharides Drive Salmonella Gut Colonization in a Context-Dependent MannerPreprint

Schubert, C., Nguyen, B. D., Sichert, A., Näpflin, N. C., Sintsova, A., Feer, L., Näf, J., Daniel, B. B. J., Steiger, Y., von Mering, C., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.08.06.606610 · Cited by 5

Antibiotic use in the past 8 years and gut microbiota compositionPreprint

Baldanzi, G., Larsson, A. H., Sayols-Baixeras, S., Dekkers, K. F., Hammar, U., Nguyen, D. T., Graells, T., Ahmad, S., Volpiano, C. G., Méric, G., et al. (2024) · medRxiv · doi:10.1101/2024.10.14.24315441 · Cited by 5

Metabolite-mediated interactions and direct contact between Fusobacterium varium and Faecalibacterium prausnitzii

Hosomi, K., Maruyama, S., Matsuoka, T., Furuta, M., Tojima, Y., Uchiyama, K., Morita, M., Kawashima, H., Kobayashi, T., & Kunisawa, J. (2025) · Microbiome · doi:10.1186/s40168-025-02168-w · Cited by 4

Mechanism of the Gut Microbiota Colonization Resistance and Enteric Pathogen Infection

Khan, I., Bai, Y., Zha, L., Ullah, N., Ullah, H., Shah, S. R. H., Sun, H., & Zhang, C. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.716299 · Cited by 291

Control of pathogens and pathobionts by the gut microbiota

Kamada, N., Chen, G. Y., Inohara, N., & Núñez, G. (2013) · Nature Immunology · doi:10.1038/ni.2608 · Cited by 1,625

Gut microbiota: Role in pathogen colonization, immune responses, and inflammatory disease

Pickard, J. M., Zeng, M. Y., Caruso, R., & Núñez, G. (2017) · Immunological Reviews · doi:10.1111/imr.12567 · Cited by 1,699

Interbacterial mechanisms of colonization resistance and the strategies pathogens use to overcome them

Sorbara, M. T., & Pamer, E. G. (2018) · Mucosal Immunology · doi:10.1038/s41385-018-0053-0 · Cited by 352

Pathogen Colonization Resistance in the Gut and Its Manipulation for Improved Health

Pickard, J. M., & Núñez, G. (2019) · American Journal Of Pathology · doi:10.1016/j.ajpath.2019.03.003 · Cited by 68